Since I am also going to be doing commute-type riding more than long rides (~20-25min one way, with occasional longer rides as I can fit them into my schedule), it seems like the hotter plug would probably be better, correct?
Yes, that's correct. Spark plugs are designed to do their best work at a certain temperature, and hotter plugs will soak up more heat. If you're doing a lot of riding at high RPM, the engine makes more heat and a colder plug will resist it to keep itself at the right temperature. For what you're doing, stick with the hotter plug. The generic NGKs that Honda sells as OEM seem to do well. The iridium plugs just last longer. Speaking of those, if you're going to use them, get the standard tip, as the IX may produce a different spark than the engine was designed for.
The plugs are obviously needing to be replaced as they have a significant amount of deposits on them - do I need to have the fuel/air mix adjusted to prevent this?
As Paul said, the FI system on the ST is closed-loop, programmed based on the assumption that the factory exhaust is fitted and is not reprogrammable. Dynojet had to give up when a firmware change in 2004 rendered the Power Commander useless. I have the stock exhaust and have never pulled the plugs on an ST with anything else, so I can't say whether the ECM will compensate properly for the aftermarket pipes. Based on how aggressively it fights modifications, I'm inclined to say that it does.
Your plugs do look a bit nasty, but if you don't know the service history, they could just be old. I wouldn't worry about the oil unless you're finding signs that the sealing washer is letting it escape.
Is there a recommended fuel additive I could use to start cleaning this junk out of my engine? In my 4-wheel vehicles, I use the BG line of products, such as the 44k fuel system cleaner, when I get the vehicle and then yearly thereafter, but I don't know if it's OK to use in this small of an engine.
I use 8 ounces of Sea Foam in a tank. 44K is pretty much the same thing everybody else is selling (petroleum distillates, mineral spirits and sometimes alcohol) at a much higher price (an 11-ounce can of 44K runs about $17 where a 16-ounce can of Sea Foam can be had for about half that). Displacement doesn't factor into it.
Make sure everything in the intake path up to the throttle bodies is clean and unobstructed, especially the air filter. (If you look at the butterfly valves and see what looks like black goop on the edges, that belongs there. Don't try to clean it and don't spray anything with carb cleaner.) Then install a fresh set of plugs and run a couple of tanks of treated fuel through it, doing as many highway miles as you can swing. You want to get the engine good and hot and give the fuel system cleaner some time to do its work. Resist the temptation to judge any improvements in performance while there's cleaner in the system; my unscientific observation has been that the stuff burns a lot better than straight gas.
--Mark
